## `summarise()` has grouped output by 'patient', 'age_at_sample_exact', 'age_at_sample', 'DOB', 'DATE_OF_DIAGNOSIS'. You can override using the `.groups` argument.
## Joining, by = "PDID"
| patient | ID | age_at_sample_exact | cell_type | phase | BaitLabel | |
|---|---|---|---|---|---|---|
| 2 | PD5117 | PD5117d | 68.65708 | WGS | Recapture | d |
| 3 | PD5117 | PD5117e | 80.09309 | WGS | Recapture | e |
| 1 | PD5117 | COLONY82 | 81.92471 | BFU-E-Colony | Colony | NA |
tree=plot_basic_tree(PD$pdx,label = PD$patient,style="classic")
The nodes in this plot can be cross-referenced with nodes specified in subsequent results. The plot also serves to give an idea of what the topology at the top of the tree looks like.
tree=plot_basic_tree(expand_short_branches(PD$pdx,prop = 0.1),label = PD$patient,style="classic")
node_labels(tree)
Note that the different colours on the tree indicate the separately fitted mutation rate clades.
##
## Random-Effects Model (k = 1; tau^2 estimator: REML)
##
## logLik deviance AIC BIC AICc
## 0.0000 -0.0000 4.0000 -Inf 16.0000
##
## tau^2 (estimated amount of total heterogeneity): 0
## tau (square root of estimated tau^2 value): 0
## I^2 (total heterogeneity / total variability): 0.00%
## H^2 (total variability / sampling variability): 1.00
##
## Test for Heterogeneity:
## Q(df = 0) = 0.0000, p-val = 1.0000
##
## Model Results:
##
## estimate se zval pval ci.lb ci.ub
## 17.1726 0.3777 45.4682 <.0001 16.4323 17.9128 ***
##
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## `summarise()` has grouped output by 'patient'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'patient'. You can override using the `.groups` argument.
| node | driver | status | child_count | type | colony_count | mean_lambda_rescaled | correction | sd_rescaled | lb_rescaled | ub_rescaled | median_rescaled | p_lt_wt |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| -1 | WT | 1 | -1 | local | 39 | 17.17255 | 1.013181 | 0.1426444 | 16.89712 | 17.45471 | 17.17156 | NA |
| 94 | JAK2 | 1 | 49 | local | 49 | 17.88570 | 1.013181 | 0.2606240 | 17.39160 | 18.41653 | 17.87925 | 0.006225 |
All ages are in terms of post conception years. The vertical red lines denote when colonies were sampled and blue lines when targeted follow up samples were taken.
| patient | node | driver | child_count | lower_median | upper_median | lower_lb95 | lower_ub95 | upper_lb95 | upper_ub95 | N | group | age_at_diagnosis_pcy | max_age_at_sample | min_age_at_sample |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| PD5117 | 94 | JAK2 | 49 | 0.0550276 | 11.50331 | 0.0315347 | 0.1186367 | 9.918325 | 13.22771 | 3 | JAK2 | 65.68378 | 82.65298 | 69.38535 |
| PD5117 | 125 | TET2 | 2 | 25.2104523 | 42.72000 | 23.2099085 | 27.2509644 | 40.410834 | 45.00196 | 3 | TET2 | 65.68378 | 82.65298 | 69.38535 |
| PD5117 | 135 | 9pUPD | 3 | 20.4197451 | 46.21496 | 18.5837464 | 22.3284887 | 44.089027 | 48.25920 | 3 | 9pUPD | 65.68378 | 82.65298 | 69.38535 |
## Timings using the Clade Specific Rates
| label | node | het.sensitivity | chr | start | end | nhet | nhom | mean_loh_event | lower_loh_event | upper_loh_event | t_before_end | t_before_end_lower | t_before_end_upper | kb | count_in_bin | count_se | pmut | pmut_se | xmean | xse_mean | xsd | x2.5. | x50. | x97.5. | xn_eff | xRhat | lmean | lse_mean | patient | driver3 | child_count |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 9pUPD_A | 135 | 0.9597 | 9 | 14690 | 28231047 | 0 | 1 | 40.55 | 28.28 | 46.04 | 5.654 | 0.1594 | 17.92 | 28200000 | 5561 | 74.57 | 0.012145 | 0.0001629 | 0.7806 | 0.0011827 | 0.1879 | 0.30448 | 0.8325 | 0.9938 | 25243 | 1 | 5.475 | 0.0004857 | PD5117 | 9pUPD:JAK2 | 3 |
| 9pUPD_B | 46 | 0.9108 | 9 | 14690 | 28231047 | 10 | 2 | NA | NA | NA | NA | NA | NA | 28200000 | 5561 | 74.57 | 0.012145 | 0.0001629 | 0.2736 | 0.0007983 | 0.1218 | 0.07196 | 0.2625 | 0.5373 | 23271 | 1 | 11.104 | 0.0009423 | NA | NA | NA |
| 9pUPD_C | 48 | 0.8862 | 9 | 14690 | 15677291 | 2 | 1 | NA | NA | NA | NA | NA | NA | 15600000 | 2708 | 52.04 | 0.005914 | 0.0001136 | 0.5168 | 0.0012623 | 0.2036 | 0.11852 | 0.5260 | 0.8736 | 26029 | 1 | 7.197 | 0.0008770 | NA | NA | NA |
Here we exclude all local CNAs and depict as color VAF plots